Friday, December 21, 2012

The NRA is offering to help with the effort to put guns in schools. Mr. LaPierre named former Arkansas Republican congressman Asa Hutchinson to lead a National School Shield Program to help design security plans for every school in the country.

Because, as Mr. LaPierre put it: “The only thing that stops a bad guy with a gun is a good guy with a gun.”

If there is a one statement that sums up the political divide in America, that may be it.

Here's the video of the NRA press conference.

And here's part of the transcript ...

With all the foreign aid, with all the money in the federal budget, we can’t afford to put a police officer in every school? Even if they did that, politicians have no business — and no authority — denying us the right, the ability, or the moral imperative to protect ourselves and our loved ones from harm.

Now, the National Rifle Association knows that there are millions of qualified active and retired police; active, reserve and retired military; security professionals; certified firefighters and rescue personnel; and an extraordinary corps of patriotic, trained qualified citizens to join with local school officials and police in devising a protection plan for every school. We can deploy them to protect our kids now. We can immediately make America's schools safer — relying on the brave men and women of America’s police force.

The budget of our local police departments are strained and resources are limited, but their dedication and courage are second to none and they can be deployed right now.

I call on Congress today to act immediately, to appropriate whatever is necessary to put armed police officers in every school — and to do it now, to make sure that blanket of safety is in place when our children return to school in January.

There are about 130,000 schools in America. Let's say we find 130,000 people who are willing and able to use a gun to kill anyone who tries to get into the school. Imagine that many of them are "patriots" who belong to the National Rifle Association. They'll probably be working for close to minimum wage. A bored, underpaid, cowboy with a loaded gun in every school.

Here's a video of Michael Ruse criticizing Richard Dawkins for being too simplistic in his attack on belief in god(s). What Ruse is saying is that theologians have a much more sophisticated view of religion than Dawkins admits. It goes without saying that really good philosophers, like Ruse, understand the sophisticated version of Christian apologetics so they would never write a book like The God Delusion.

Ruse gives us an example of the worst form of accomodationism. Beginning at 2:11, Ruse treats us to a defense of the cosmological argument for the existence of god. Here's his (Ruse's) brief description.

1. Everything has a cause.
2. The world is a thing therefore the world must have a cause.
3. Call it god.

This is somewhat simplistic (), a more sophisticated version can be found on Wikipedia (above) or at the Stanford Encyclopedia of Philosophy: Cosmological Argument.

I've been waiting for a response from Ann Gauger or any of the other IDiots. I've been waiting to see how they twist the meaning of "population genetics" to fit what she says in the video. I've been waiting to see how they defend her words on tree-making given the criticism on Sandwalk and elsewhere.

Incidentally, it turns out that the "laboratory" in the background of the video is a stock photo from Shutterstock and not an actual lab where Ann Gauger works. Here's the video so you can see what I'm talking about.

David Klinghoffer has finally responded to the criticism in a post on Evolution News & Views: Scandal! Gauger Filmed in Front of Green Screen. As you can see from the title, he is most upset about the use of a fake lab ... or rather he's upset about being discovered and exposed by Richard B. Hoppe at Panda's Thumb and Casey Johnston at Ars Technica.

But what about the scientific criticism of what Ann Gauger is actually saying in the video?

Klinghoffer has an answer ....

It's hard to believe that Miss Johnson, who writes for Ars Technica ("a trusted source for technology news, tech policy analysis, breakdowns of the latest scientific advancements"), is unaware of these things. So too Richard Hoppe. The most likely explanation for their posing at the game of "Gotcha!" is that they can't answer Dr. Gauger's arguments, which are given in full in a recent brief book co-authored by Gauger, Doug Axe and Casey Luskin, Science and Human Origins. We would be happy to send a review copy to Ars Technica.

Gauger, a PhD in developmental biology who was a post-doctoral fellow at Harvard, has the science on her side. It's a typical Darwinist feint: When you don't have the arguments and you don't have the science, change the subject and pile on the red herrings. Casey Johnson, who dismisses our little video as a "nonsensical rant," can't reply to Dr. Gauger on the merits. If she could, she would.

David Klinghoffer reads Sandwalk so he knows how real scientists deal with the nonsense being spouted by Ann Gauger. I suspect he would rather focus on the "red herring" than defend the bad science in the video.

he CSC Seminar on Intelligent Design in the Natural Sciences will prepare students to make research contributions advancing the growing science of intelligent design (ID). The seminar will explore cutting-edge ID work in fields such as molecular biology, biochemistry, embryology, developmental biology, paleontology, computational biology, ID-theoretic mathematics, cosmology, physics, and the history and philosophy of science. The seminar will include presentations on the application of intelligent design to laboratory research as well as frank treatment of the academic realities that ID researchers confront in graduate school and beyond, and strategies for dealing with them. Although the primary focus of the seminar is science, there also will be discussion of the worldview implications of the debate over intelligent design. Participants will benefit from classroom instruction and interaction with prominent ID researchers and scholars. Past seminars have included such speakers as Michael Behe, Stephen Meyer, William Dembski, Jonathan Wells, Paul Nelson, Jay Richards, Douglas Axe, Ann Gauger, Richard Sternberg, Robert Marks, Scott Minnich, and Bruce Gordon. The seminar is open to students who intend to pursue graduate studies in the natural sciences or the philosophy of science. Applicants must be college juniors or seniors or already in graduate school.

Do you have a commitment to truth and to following the evidence where it leads? Do you have the desire, the vision and the determination necessary to breathe new purpose into the scientific enterprise and influence its self-understanding in ways that will benefit both science and humanity? Apply to become one of a select group of students participating in this exciting workshop.

This is your chance to get up-to-date information on biochemistry and population genetics from Michael Behe and Ann Gauger! You can learn about evolution from Young Earth Creationist Paul Nelson and anti-evolutionist Jonathan Wells.

What an opportunity! I'm sure there are many Sandwalk readers who would welcome the chance to learn about Intelligent Design directly from its main proponents. This is bound to be a marvelous course, even if you're a skeptic.

The application process seems pretty straightforward. It looks like they're open to all points of view so they can have a healthy debate in a critical thinking environment.

Admission Requirements: You must be currently enrolled in a college or university as a junior, senior, or graduate student. Required application materials include (1) a resume/cv, (2) a copy of your academic transcript, (3) a short statement of your interest in intelligent design and its perceived relationship to your career plans and field of study, and (4) either a letter of recommendation from a professor who knows your work and is friendly toward ID, or a phone interview with the seminar director.

Just ignore the fact that you need a letter from a professor who's ID-friendly. I'm sure they don't mean that as way of eliminating skeptics and evolutionists. I'm sure that the phone interview is just a way of confirming that you are really interested in learning about Intelligent Design Creationism no matter what your religion.

I'm sure that any organization promoting critical thinking and "teach the controversy" would never choose their students based on whether they are already proponents of Intelligent Design Creationism.

Same goes for any organization that would support a movie like Expelled: No Intelligence Allowed ("Big science has expelled smart new ideas from the classroom.") Especially since Richard Sternberg might be one of the lecturers.

The man who is advocating gun culture is Louie Gohmert, a Republican member of the United States Congress representing the 1st Congressional District of Texas. Gun control will never be successful as long as a substantial number of Americans think like this. Gohmert won the last election (Nov. 2012) with 72% of the vote.

Change the culture. Violence is never the answer and more violence will never fix the problem. Change the culture and gun control automatically follows, as in most other countries. It's unlikely that tweaking a few gun laws will make much of a difference as long as everyone thinks it's okay to act like a gun-toting vigilante.

Monday, December 17, 2012

Last week's molecule was tetrahydrofolate, an essential cofactor in several reactions; notably the synthesis of thymidine. The winner was Jacob Troth [Monday's Molecule #195]. He should contact me by email.

This week's molecule is a very important molecule. I'm showing you two different conformations of the same molecule. You need to identify this molecule using its full and complete common name. I'm going to be strict about this, if you give me an ambiguous name you will not win.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

As most of you know, there's a reason why we call them IDiots. There's a reason why faculty members in a biology department might not get tenure if they believe most of the things you read on Evolution News & Views (sic). There's a reason why a student might get a low grade for questioning the existence of natural selection or for thinking that skin cells don't accumulate mutations.

The elected members of the Texas legislature are well aware of this discrimination against stupidity so they've taken steps to stop it. Bill HB285 "Relating to prohibiting discrimination by public institutions of higher education against faculty members and students based on their conduct of research relating to intelligent design" should do the trick, if it becomes law.

Here's the key provision,

An institution of higher education may not discriminate against or penalize in any manner, especially with regard to employment or academic support, a faculty member or student based on the faculty member’s or student’s conduct of research relating to the theory of intelligent design or other alternate theories of the origination and development of organisms.

I suppose it was inevitable that politicians in Texas would finally recognize that their children might flunk out of university.

Friday, December 14, 2012

Most of us are aware of the ENCODE publicity fiasco. The leaders of the project made some outlandish claims about the function of most of our genome in order to attract attention and make their work seem much more significant than it really is [see Sean Eddy on Junk DNA and ENCODE].

Many scientists tried to set the record straight and they pretty much succeeded, at least in the scientific community. Most scientist now know that the case for junk DNA is a lot stronger than they thought.

Unfortunately, the criticisms didn't get much publicity and the average person is left with the impression that most of our genome has an important function, even if we don't know exactly what that function is. This means that good science writers have to work harder to educate the public about the true state of our genome.

The relationship between our genome and disease is far more complicated than originally anticipated. Indeed, the more we learn about the human genome, the less we seem to know. For example, results from a major international initiative to explore all the elements of our genome (the ENCODE project) found that, despite decades-old conventional wisdom that much of our genome was nothing but “junk DNA,” as much as 80 per cent of our genome likely has some biological function. This work hints that things are much more convoluted than expected. So much so that one of ENCODE’s lead researchers, Yale’s Mark Gerstein, was quoted as saying that it’s “like opening a wire closet and seeing a hairball of wires.”

Statements like this from someone who is supposed to be knowledgeable about such issues show us that the ENCODE fiasco has far-reaching consequences. The misleading statements by Ewan Birney and others will take years to undo. It's all the more reason to criticize Nature and Science for aiding and abetting the spread of this false information.

How can we expect people like Timothy Caulfield to understand the science if the leading journals get it wrong?

Paul Nelson has been challenging the pervasiveness of adaptationism by pointing out that many evolutionary biologists promte nonadaptive evolution. See the discussion and comments on Jerry Coyne's blog website: A Marshall McLuhan moment with creationist Paul Nelson. Nelson has been accused, falsely, of claiming that some evolutionary biologists deny that natural selection is an important mechanism in evolution.

Paul Nelson doesn't deny that natural selection is a real phenomenon. He may be an IDiot (and a YEC) but he's not THAT stupid. On the other hand, one didn't have to wait too long before getting confirmation that some other IDiots really are THAT stupid.

And guess what? They are allowed to post on the main Discovery Institute blog, Evolution News & Views (sic)!!! You have to read How "Real" Is Natural Selection? by Tom Bethell ... otherwise you'd never believe me.

Thursday, December 13, 2012

Udo Schüklenk is a Professor of Philsophy at Queen's University in Kingston, Ontario, Canada. His specialty is bioethics.

Udo gave a presentation at Eschaton 2012 on Myths About Atheist Values. He covered three topics ...

1. Are atheists moral? Yes

2. Does life have meaning or purpose? No, not the same kind of meaning and purpose that theists imagine.

3. Do atheists value human life? Yes.

Udo has a blog and one of the services he provides on his blog is to teach us about bioethics. Part of this service is to expose quacks masquerading as bioethicists. It's a thankless job but someone has to do it.

Fortunately, Udo concentrates on Canadian quacks so you won't be overwhelmed. There are only a few hundred, mostly doctors.

Perhaps Canada's most famous quack bioethicist is Margaret Somerville, a Professor of Law at McGill University, (Montreal, Quebec, Canada). She's best known for her opposition to same-sex marriage and she's been advertised on television and in newspapers as a bioethicist who has rational views on the dangers of legalizing same-sex marriage. (She wasn't very persuasive since same-sex marriage is legal in Canada.}1

Margaret Sommerville didn't like their recommendations. She claims that further legalization of euthanasia will lead to people being killed against their will.

Here's how Udo deals with that issue ...

Evidence has never been Ms. Somerville's strongest point. So, without any evidence to back up her claims she declares on the Catholic website, "One of the things that's wrong with respect to Justice (Lynn) Smith's judgment (in Carter v. Attorney General of B.C.) is that she purports to review the use of euthanasia and physician-assisted suicide in the jurisdictions that have legalized it. She said there is no problem, there is no slippery slope. Well, that's simply not right factually." It turns out, in our Report on end of life decision-making in Canada we reviewed the empirical evidence on the slippery slope matter and concluded that there is no evidence that assisted dying leads us down slippery slopes to unwanted killings. Of course, we reviewed evidence, Ms Somerville is in full preaching mode.

I like this guy! He thinks that real, scientific, "evidence" is an important part of any debate.

1. We're anxiously waiting to see if her predictions about kids of gay parents being traumatized will come true.

Tuesday, December 11, 2012

Can you go from some simple character to a more complex feature without invoking natural selection? Yes, you can. Complex features can evolve by nonadaptive means. Just think of our complex genome and read The Origins of Genome Architecture by Michael Lynch.

This is an important point. You can't just assume, without question, that a complex trait must be an adaptation and must have arisen by natural selection. That applies to molecular complexes and also to complex behavior.

Monday, December 10, 2012

In my opinion, science is a way of knowing characterized by a requirement for evidence, healthy skepticism, and rationality. "Knowing" refers to something called "universal truth" because knowledge has to be more than just something that an individual believes is true.

I'm not aware of any other way of knowing that has produced something we can reliably classify as "knowledge" by any reasonable criteria. From time to time I've asked for examples but nobody has been able to provide any example of "universal truth" (i.e. knowledge) that has been reached by any other process.

Consider history for example. We know with a high degree of reliability that Abraham Lincoln was the president of the United States in 1863. I did not arrive at this knowledge through scientific means. I know it because someone told me, and they in turn learned it from someone else, who in turn learned it from someone else back to the actual people who witnessed first-hand a man who called himself “Abraham Lincoln” sitting in the White House in 1863 and acting for all the world like he was the president of the United States.

Consider geography. I have never been to Russia, but I am quite certain that Moscow is the capital of that country. I did not arrive at this knowledge through scientific means either.

If timothya will stop and think a moment, he will realize that practically everything he knows he knows because someone told him, not because the truth of the proposition has been confirmed by science.

I guess that settles it. If lots of people tell you that god exists then it must be true. Epistemology is finished and the demarcation problem is solved.

Lots of people tell me that Intelligent Design Creationists aren't very bright.

The main problem with the adaptationist approach is identifying adaptations. Is something really an adaptation or are there other explanations? Part of the answer involves providing evidence that the behavior has a specific genetic component.

I don't think those problems are satisfactorily addressed in this review in spite of Jerry's recommendation. If this is the best the field has to offer then it's in real trouble.

Here's an example from that paper of the "best" kind of science.

The science of confirming and falsifying hypotheses, of course, is typically more complex than these examples indicate. Often a hypothesis is embedded within a larger theoretical network. For example, one evolutionary prediction is that women will prefer men as potential mates who express a willingness to invest in them and their offspring (Buss, 1995). This is derived from the hypothesis that in paternally investing species, females will use cues to a man’s willingness to invest as a criterion for mate selection. In turn, this hypothesis is derived from parental investment theory, which posits that the sex that invests more in its offspring will be the choosier sex when selecting mates (Trivers, 1972). Finally, the logic behind parental investment theory is derived from inclusive fitness theory (Hamilton, 1964a, 1964b), the modern formulation of evolution by natural selection. As in all realms of psychological science, the evaluation of each evolutionary psychological hypothesis, as well as the broader theories within which they are embedded, rests with the cumulative weight of the empirical evidence.

I've always been puzzled about the evolutionary significance of mate selection in humans. Whenever I look at genealogical records I'm impressed by the fact that almost all men and women who reach maturity seem to find a mate. This jibes well with my personal experience since all of my friends who wanted to live with a partner succeeded in finding one. I wonder how powerful these mate selection criteria can be if there aren't significant numbers of people don't succeed in mating. Where are the ugly mean and women who couldn't find a mate?

Was the situation any different among small groups of hunter-gathers in the distant past? Did each small group have a few individuals that nobody wanted to mate with? Wouldn't that have to be the case if you are going to postulate significant adaptive value to criteria such as facial features, body outline, youthful appearance etc.?

I understand that there are studies showing that men and women in different cultures will prefer certain physical characteristics in their mates. What I don't know is whether this actually translates into mate selection when the time comes to form a stable partnership (e.g. get married). It doesn't seem like it to me otherwise almost all wives would look like Marilyn Monroe.

If women are the choosers then why aren't there lots of single men who will never have children even though they want to? Where are the losers in our societies? How common were they in the past?

What about hypothesizing that we all dream about the appearance of the ideal mate but that when it comes time to make a choice we put our emphasis on other characteristics (e.g. availability)? Maybe our preferences aren't really adaptations at all? Was that one of the hypotheses that was considered or do evolutionary psychologists jump immediately to adaptive story-telling?

Last week's molecule was allantoin, the breakdown product of uric acid that's found in the urine of mammals. Other animals can degrade allantoin to more simple compounds but mammals have lost the genes for this pathway. The winners were Paul Clapham and Jacob Troth [Monday's Molecule #194]. They should contact me by email.

This week's molecule is a ubiquitous and essential molecule in all species. Give the common name but be sure you don't confuse it with other, very similar, molecules.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

My friends and I were talking about the purpose of education over dinner on Saturday night. This video criticizes one side of the issue; namely, the idea that the purpose of education is to prepare you for a job. It should not be the goal of education.1

Apparently the high command at TED has woken up to the fact that they are being bamboozled by pseudoscientists. Phil Plait of Bad Astronomy alerts us to a letter that they recently sent out to all TEDx organizers [TEDx Talks: Some Ideas Are Not Worth Spreading]. (I love his title!)

In light of a few suspect talks that have come out of the TEDx movement — some of which we at TED have taken action to remove, some being examined now — and this recent thread on Reddit [http://www.reddit.com/r/science/comments/1444lm/the_ted_name_is_being_dragged_through_the_mud_in/], we feel it is important to reach out to all TEDx organizers on the topic of bad science and pseudoscience.

Please know this above all:
It is your job, before any speaker is booked, to check them out, and to reject bad science, pseudoscience and health hoaxes.

Vetting your speakers is hard work, and can lead to uncomfortable moments. But as TEDx organizers, your audience’s trust is your top priority, over and above any other personal or business relationship that may have brought this speaker to your attention. It is not your audience’s job to figure out if a speaker is offering legitimate science or not. It is your job.

The consequence of bad science and health hoaxes are not trivial. As an example, Andrew Wakefield’s attempt to link autism and vaccines was exposed as a hoax last year. But while his work was being investigated, millions of children went without vaccines, and many contracted deadly illnesses as a result.

We take this seriously. Presenting bad science on the TEDx stage is grounds for revoking your license.

Apparently TED will take down videos that spread pseudoscience. That explains why I was having so much trouble finding examples.

Shapiro seems to be really upset that NCSE would choose someone like me to review his book. He opens his rebuttal with ...

Before I saw Laurence A Moran’s book review (Moran 2012), I wrote the following: “It is a shame that NCSE chose Larry Moran to review my book; not because of anything he said in the review but because he is hostile to new ideas and perspectives.”

A year ago, Moran posted a piece entitled “Physicists and biologists” on his Sandwalk blog [Physicists and Biologists1]. In this post, he ridiculed the enthusiasm I expressed in the book for physicists coming into evolutionary studies and bringing new skills and new ideas.

Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism and ecology. That’s just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.

What a great way to make new friends for evolution science—equating physicists with creationists and calling them “equally ignorant”!

Friday, December 07, 2012

One of the Saturday morning sessions at Eschaton 2012 was on science education. Eugenie Scott started off with a survey of various states (in the USA) that are passing laws promoting creationism. In my presentation I tried to explain the scientific facts that we know for sure then I described an example of Intelligent Design Creationist stupidity showing that they really have no idea what they are talking about. See: Breaking News: IDiots Don't Understand Genomes or Biology. PZ Myers finished of with a depressing summary of the state of science education in the USA.

In my talk I explained that I preferred a broad definition of science, one that emphasizes science as a way of knowing. My definition encompasses the activities of everyone who seeks knowledge and that includes people working in fields outside of the traditional science disciplines.

Eugenie Scott prefers a more restricted definition of science, one that refers to the activities of biologists, chemists, physicists, and geologists. Eugenie thinks there are other ways of knowing and she supports the idea that the actions of scientists are constrained by the rule of methodological naturalism.

I met many interesting people at Eschaton 2012 in Ottawa. One of them was Ian Cromwell who gave a talk about racism on Sunday morning. Ian thinks that the skeptic/atheist movement ought to pay more attention to racism and he made his point by teaching us how to recognize zombies and racists.

Ian has a degree in statistics and epidemeology from Queen's University (Ontario, Canada) and he now works in Vancouver (British Columbia, Canada). He has a blog called The Crommunist Manifesto on Freethought Blogs. His blog deals mostly with racism issues.

Here's a video of a recent talk he gave in Vancouver (Part 1 of 5).

I really enjoyed Ian's presentation except for one small comment he made. He said something like, "There's no meaningful distinction between human races." When I asked him about this after his talk, he seemed to defend the proposition that human races don't exist. The comments on his blog suggest that we could have a productive discussion about the meaning of the word "race." See: #Eschaton2012: some additional reflections where he says ...

The thesis statement of my talk: that skepticism can and should be applied to the topic of race, seemed to strike the crowd as pretty non-controversial, which was nice. The lion’s share of the questions in the subsequent panel went to me, suggesting to me that the topic of race is one that is underexplored but sorely wanted within the skeptical/freethinking movement. There was an exchange with Larry Moran after my talk was over that I anticipate will turn into a brief back-and-forth between our two blogs as we sort out the biological underpinning of race and what those mean in the real world.

My position is that the term "race" is used frequently to describe sub-populations of species, or groups that have been genetically isolated from each other1 for many generations. By this definition, races exist in humans just as they do in many other species.

The genetic evidence shows clearly that Africans form a distinctive, but somewhat polyphyletic, group that differs from the people living outside of Africa. Amongst the non-Africans, we recognize two major sub-groups; Europeans and Asians. I see no reason why these major sub-populations don't qualify as races in the biological sense. lease read: Do Human Races Exist?.

I don't think that denying the existence of races is going to make racism go away. Nor do I think that accepting the existence of biological races is going to foster racism.

1. Genetically isolated does NOT mean there's no gene flow between the groups. Is there was none, they would be different species. Please don't use the silly argument that the existence of hybrids disproves the concept of human races.

Thursday, December 06, 2012

One of the remarkable things about kooks is that they are incredibly resistant to learning from their mistakes. James Shapiro gives us a fine example in one of his latest articles on The Huffington Post where he tries to convince us that the old definition of "gene" has outlived its usefulness. According to Shapiro, "DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function."

Really? While we all can agree that there's no definition of "gene" that doesn't have exceptions, we can surely agree that some definitions work pretty well. I've argued that defining a gene as, "a DNA sequence that is transcribed to produce a functional product" works well in most cases [What Is a Gene?].

Let's see how James Shapiro handles this problem.1 He says,

The identification of DNA as the key molecule of heredity and Crick's Central Dogma of Molecule Biology [Crick 1970] initially seemed to confirm Beadle and Tatum's "one gene -- one enzyme" hypothesis.

It's not a very impressive list. Since the discussion about evolutionary psychology is heating up again, it's time to send out another request. What are the very best papers in the field—the ones you are proud to point to whenever any criticizes evolutionary psychology? PZ Myers also wants to know [αEP: Shut up and sing!. John Wilkins would also like some examples since he's just launched a series of posts defending evolutionary psychology [Evopsychopathy 1. Conditions for sociobiology].

The remarkable—a word that can be read in many different ways—2012 student protests in Quebec have stirred memories of the activist campuses of yesteryear. For faculty members introduced to the academy in the era of student activism, anti-Vietnam War protests, and general social unrest, the recent quietude of the Canadian university system has been disturbing. Universities had been transformed in the 1960s from comfortable retreats into agents of intellectual foment, social change, and political action. For a time, it appeared that the imperatives of the academy had aligned with a commitment to social justice to create a system almost ideally set to lead Canada’s transformation.

Universities had long stood apart intellectually from the Canadian mainstream, but finally, in the 1960s, began to reflect society at large. The humanities and social sciences expanded rapidly. Women, minorities, immigrants and working class Canadians came to campuses in record numbers and, later, showed up at the front of the classroom. They brought new perspectives on the issues of the day, challenging the patriarchal, middle-class hegemony that had dominated Canadian universities for generations. With some exceptions, faculty members and administrators stood behind student radicals and protestors. Many faculty members used the classroom and their writing to support hitherto unpopular causes. Universities were often at the vanguard of protests against the Vietnam War and in favour of the rights of women, Aboriginals, LGBT individuals, and minorities.

I was a student in the 1960s. Universities are no longer like that. What happened?

Canadian campuses have become distressingly quiet. It is not that the universities are without dissenters from all points on political and social spectrums. Many of the country’s most radical, creative, and outspoken commentators work or study at universities and use the campus as a pulpit. This is how it should be. But the preoccupation with practicalities—work, careers, salaries, and the commercialization of research—has transformed Canadian universities into calm, largely dissent-free places, with the greatest debates often saved for battles between faculty and students and the campus administrators. There are no structural or legal impediments to greater engagement. There is nothing stopping students and faculty from speaking out, no grand tribunals determined to impose punishments on those who challenge the status quo. We have self-regulated ourselves into near silence, and our students and the country suffer from the quiet as much as university faculty. It is more than nostalgia that brings one to yearn for days of activism and protest; it is, instead, the realization that the ideas, talent, energy and resources of the academic could and should be used to change our country and our world for the better.

Tuesday, December 04, 2012

Sean Eddy is a bioinformatics expert who runs a lab at the Howard Hughes Medical Institute (HHMI) Janelia Farm Research Campus in Virginia (USA).1 Sean was one of the many scientists who spoke out against the ENCODE misinterpretation of their own results [ENCODE says what?].

Most people now know that ENCODE did not disprove junk DNA (with the possible exception of creationists and a few kooks).

Recently, the ENCODE project has concluded that 80% of the human genome is reproducibly transcribed, bound to proteins, or has its chromatin specifically modified. In widespread publicity around the project, some ENCODE leaders claimed that this biochemical activity disproves junk DNA. If there is an alternative hypothesis, it must provide an alternative explanation for the data: for the C-value paradox, for mutational load, and for how a large fraction of eukaryotic genomes is composed of neutrally drifting transposon-derived sequence. ENCODE hasn’t done this, and most of ENCODE’s data don’t bear directly on the question. Transposon‑derived sequence is generally expected to be biochemically active by ENCODE’s definitions — lots of transposon sequences are inserted into transcribed genic regions, mobile transposons are transcribed and regulated, and genomic suppression of transposon activity requires DNA‑binding and chromatin modification.

The question that the ‘junk DNA’ concept addresses is not whether these sequences are biochemically ‘active’, but whether they’re there primarily because they’re useful for the organism.

I hope everyone enjoyed their holiday dinosaur this Thanksgiving, and thank you joining me in this delightful excursion out into the wide wonderful world of ideas and expressions in evolution.

As it turns out, I did enjoy eating dinosaur on Thanksgiving but it was so long ago (Oct. 8) that I've forgotten what it tasted like.

Enjoy your tour of Mt. Improbable!

The next Carnival of Evolution (September) will be hosted by Genome Engineering. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.

Last week's molecule was N-(2-aminoethyl)glycine, a molecule that has been used to build artificial DNA molecules. The winner was Michael Rasmussen [Monday's Molecule #193].

This week's molecule is a real pisser. You'll have to give the complete, unambiguous, formal name AND explain why we don't make it.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

It's really hard to maintain one's reputation as a curmudgeon. John Wilkins is having a particularly tough time these days since most of his poss are quite reasonable and rational. I even agree with him on most days.

Monday, December 03, 2012

One of the highlights of Eschaton 2012 was taking PZ Myers to the Elgin Street Grill for poutine. He had the plain, ordinary version diluted with a chicken burger. I had the chili poutine.

Other highlights included his two talks. The one on Saturday morning was about the sorry state of science education in the United States. That was depressing.

PZ's talk on Saturday evening was at the Canadian Museum of Natural History, just around the corner from the hotel. There were about 200 people in the audience. He tackled a very difficult topic, the role of chance in evolution. Naturally he covered random genetic drift but most of his talk was about coalescent theory because he wanted to explain some recent results from the sequence of the gorilla genome (Scally et al. 2012).

The authors of that paper report that, "In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other." PZ explained why this is exactly the result you would expect. (See his blog post at: A tiny bit of knowledge is a dangerous thing.)

He also pointed out that the Intelligent Design Creationists got all excited about this result, thinking that it overthrows the theory of evolution and proves the existence of God. (I exaggerate slightly, but you get the point!) What this means if that the IDiots really don't understand evolution.

While we don't expect everyone to see immediately why 30% of our genes could be more similar to gorilla genes than to chimp genes, we do expect those who criticize evolution to have a better understanding. Instead, what we see is that those "experts" who post at Evolution News & Views (sic) don't even have an introductory college level understanding of evolution. Their ignorance of evolution produces some remarkably stupid posts on that blog—the website of the Discovery Institute.

PZ took on a challenging task but he succeeded better than I could have imagined. While the audience didn't follow all of the explanation, they could see that it was based on solid evidence and theory. Many of them learned for the first time about chance in evolution and that's a plus, in my opinion.

Thursday, November 22, 2012

Just when you think they couldn't get more stupid, along comes some IDiot to prove you wrong. Here's the latest from an anonymous contributor at Evolution News & Views [Your Genome? Which One?].

A new finding about DNA differences in somatic cells overthrows a common assumption and might have dramatic implications for evolutionary studies.

Young's Law (from Murphy's catalog of perverse tendencies in nature) states that all great discoveries are made by mistake. A corollary is that the greater the funding, the longer it takes to make the mistake, but we won't go there. Anyway, a team of Yale scientists wasn't looking to overturn a huge assumption in genetics -- but they did. The ripple effects of their discovery remain to be seen.

We've all been told that every cell in our body has a copy of our unique genetic code. That's one of those simplistic beliefs that sounds sensible but is almost impossible to check. Doesn't the whole body arise from cell divisions of a single zygote with its unique genetic code? Yes, but it doesn't necessarily follow that the genes in cells downstream don't get modified. That was just assumed....

"Somatic mosaicism" is jargon for the finding that genomes differ from cell to cell -- not only in copy number variations (CNV's), but in single nucleotide polymorphisms (SNP's). The assumption that you have one genome is thus falsified. You have lots of genomes!

Okay, let's take a poll.

How many of you thought that mutations such as nucleotide substitutions, deletions, and insertions, could never take place during the thousands of generations that give rise to our somatic cells? (How were they supposed to be suppressed?)

How many of you thought that all of our cells, including red blood cells, contain copies of our unmodified genome?

How many of you thought that there were no polyploid cells in our liver?

How many of you thought that B cells, and T cells (and others) contain the same identical copy of our genome that's found in germ cells?

How many of you thought that spermatocytes and ovaries have exactly the same genome as our original zygote?

How many of you thought that cancer-causing gene rearrangements and mutations in somatic cells were impossible?

How many of you are completely ignorant of any medical problems due to genetic mosaicism?

If you answered "yes" to all of those questions then, congratulations!, you're as smart as an IDiot.

Sheeesh!

One thing is clear at this stage: the assumption that each individual has a unique genome has been overthrown to some extent. Think how this might impact common evolutionary studies. For years, evolutionists have claimed small differences between human and chimpanzee genomes. What if the percent difference is a function of the source cells used? Remember, the Yale team found differences between cells in the same organ -- human skin. If the percent difference grows or shrinks depending on the source, any conclusions about human-chimp similarities would prove unreliable.

The nameless people at Evolution News & Views (sic) didn't like my comments about Michael Behe. Naturally they focus right in on defending the IDiot science (not!) [Giving Thanks for Minority Opinions]. (The reference to "thanks" is in honor of today's American Thanksgiving holiday.)

When in the future they write the history of modern biology, if it turns out that contemporary ID theorists were onto something big, then Michael Behe's name will figure very prominently as one who helped launch the intelligent-design revolution.

When that history is written, whatever fate holds in store for ID, no one thinks that University of Toronto biochemist Larry Moran's name will figure prominently in any account as a thinker of great stature or influence.

So there's some irony in Moran's patronizing three-part series, at his blog Sandwalk blog, about meeting Mike Behe when the latter came to visit and speak recently in Toronto. Moran is full of condescension and, sticking to the science as always, carefully points out the discrepancy in physical stature between himself and Behe where Moran does have the advantage -- "He's a lot shorter than I imagined but otherwise looks just like his photos." Moran includes a photo of himself leaning over Behe with a smirk to prove the point. Well then!

Lloyd explains the problems with the adaptationist approach to the logic of research questions using a case study on the evolutionary origins of female orgasm. She points out that Gould & Lewontin were right 33 years ago when they called attention to the adaptationist bias and that things haven't changed very much.

This is an excellent example of a philosopher of biology, Elizabeth Lloyd, making a substantial contribution to science and the philosophy of science

Tuesday, November 20, 2012

A Saint-Laurent man has been charged, again, with abusing social media to threaten people who express their views online.

Dennis Markuze, 40, faces three new charges, including one alleging he violated the conditions of a sentence he received in May for the same offence. He was also charged with threatening the Montreal police officer who was investigating claims from several of Markuze’s past victims. Those victims alleged that Markuze’s threats have intensified in recent months.

In May, Markuze received an 18-month suspended sentence after pleading guilty to uttering threats toward eight people he believed to be atheists. The court was told Markuze’s problems could be attributed to drug consumption, which caused him to believe he was “the Voice of God.” As part of his sentence, he was ordered to “abstain from participating in a social network, blog and discussion forum.” But during the summer, several people contacted The Gazette to report that Markuze appeared to be ignoring the court order.

The third talk was on Friday morning (Nov. 15, 2012) in the Multifaith Centre. It was sponsored by Power to Change (formerly Campus Crusade for Christ). There were about 150 people in the audience, mostly undergraduates. I estimate that less than half were believers.

Behe gave pretty much the same talk he had given the night before. There was only time for a few questions and most of them were from skeptics. Two students challenged the science but their questions were convoluted and confusing and Behe had no trouble dismissing them. (The standard trick is to say "That's a very good question" and then suggest they could discuss it later on so that others have a chance to ask questions right now.)

One student asked about the philosophical justification for some of Behe's conclusions. It was a valid question but way over the heads of the audience. Behe gave an incorrect answer. I spoke to that student and her friends after the talk. Several of them were taking biology/evolution courses but they weren't really prepared to identify the flaws in Behe's arguments. They just knew that he had to be wrong.

This is the problem. It's just not that easy for the average person to refute the arguments of people like Michael Behe and Jonathan Wells. That's why we need to teach the controversy in school and show why their science is flawed.

Monday, November 19, 2012

Here's a propaganda video produced by the Discovery Institute. It's based on a book called The Magician's Twin edited by John G. West. John G. West is "a Senior Fellow at the Seattle-based Discovery Institute (DI), and Associate Director and Vice President for Public Policy and Legal Affairs of its Center for Science and Culture (CSC), which serves as the main hub of the Intelligent design movement."

In other words, he's one of the chief IDiots.

The video is interesting for several reasons. Not only does it have the look and feel of a 1950's American propaganda film but it mimics the same utter lack of critical thinking that characterized that genre of film. Perhaps this is intentional since the goal is to attack rationality and critical thinking and the last thing you want to do is be accused of using the very tools that lead to evils such as eugenics, evolution, atheism, and Marxism. (But see "doublethink," below.)

Behe's main talk was last Thursday evening at 7pm (Nov. 15, 2012). It was in the lecture theater were we teach medical students. The room holds about 350 students and every seat was taken. There were about 100 people sitting in the aisles and on the floor.

The gist of Behe's talk was that "Darwinism" can't explain macroevolution. The problem isn't common descent—Behe agrees that common descent is "trivial." The problem isn't natural selection—Behe doesn't have a problem with natural selection. The problem is random mutation. It's incapable of generating the required changes in a timely manner.

Last week's molecule was capsaicin, the molecule responsible for the "hot" sensation of chili peppers. There were two winners: Seth Kasowitz and Bill Gunn [Monday's Molecule #192].

This week's molecule is featured in an article that I will (hopefully) blog about in the next few days. There's a common name of sorts but you will need to supply the correct IUPAC name to win the free lunch.

Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)

Sunday, November 18, 2012

Michael Behe was in Toronto last Thursday and Friday (Nov. 15 & 16, 2012). His visit was sponsored in part by the Copernicus Group, a group of Christian men who are interested in the dispute between science and religion. I met several of them (three physicians and an engineer).

The first of Behe's talks was organized by the Copernicus Group who invited faculty and graduate students from the Dept. of Biochemistry and the Dept. of Molecular Genetics to a session at Hart House in the afternoon. Only eleven people showed up—four (five?) of them were from the Copernicus group. There were ten bottles of wine!

This was the first time I had a chance to meet Michael Behe in person. He's a lot shorter than I imagined but otherwise looks just like his photos.

Today's the day of the Santa Claus parade in Toronto. The radio tells me that one million people will be lining the parade route when the parade begins. Here's the Santa Claus fans just outside my building on Queen's Park Circle. You can see that some of them were smart enough to bring a Tim Hortons coffee.

The Intelligent Design Creationists change their stories so often that it's sometimes hard to keep up. The latest rationalization has to do with the sufficiency of random mutations. Here's the version given by Ann Gauger, Senior Research Scientist at Biologic Institute.

There's a lot of discussion about this video on the Biologic Facebook page [Biologic Institute]. Some commenters (e.g. Nick Matzke) raise the issue of neutral mutations and Gauger responds (not very well). This is one of the main problems with the current IDiot propaganda. They confuse the probability of specific, single nucleotide, beneficial, mutations at a specific binding site—which have a low probability—with the total number of possible mutations at thousands of different sites, any of which could have an effect on development. Many of the mutations could have been neutral giving rise to an enormous amount of standing variation in the population. (This makes it much more likely that you will get multiple mutations.)

Don't forget we're looking at a specific outcome (evolution of Homo sapiens from a common ancestors over 6 million years). There were thousand and thousands of other possible outcomes that could have given rise to intelligent beings (maybe smart chimps?) who would eventually spawn Intelligent Design Creationists.1 We don't know the total number of possibilities but it certainly isn't just one (1). Our species is a lottery winner and we all know that specific lottery winners are highly improbable.

1. I wonder if there are any possible pathways that would have given rise to truly intelligent beings and no IDiots?

I've been having discussion with several of my friends and colleagues about whether the activities of the Intelligent Design Creationists count as "science." My position is that much of what they do is science, especially when they criticize existing scientific explanations. It may not be very good science but that's not the question. After all, there are atheist scientists who don't do much better.

One argument is that simply criticizing current theories doesn't count as science unless you can also offer a plausible, scientific, competing model. I don't think that's a requirement. Here's an example we can discuss ...

One of the latest posts on Evolution News & Views (sic) is an article by Casey Luskin criticizing the old Urey-Miller experiment by pointing out that their origninal conditions didn't mimic the conditions on the primitive Earth [On the Miller-Urey Experiment, Wikipedia Offers a Citation Bluff]. He goes on to say that scientists still haven't shown convincingly that amino acids (and other molecules) could have formed spontaneously on Earth. Furthermore, the "chirality problem" hasn't been solved.1

Luskin correctly points out that a Wikipedia reference misrepresents the science it reports.

Is this (Luskin's article) scientific? Isn't criticism of current models and hypotheses an example of how science is supposed to work?

1. I agree that the spontaneous formation on Earth of significant amounts of amino acids, carbohydrates, and, especially, nucleotides, is extremely unlikely. That's why I support "Metabolism First." I disagree about the chirality problem—I think we have a good explanation.

I'm not going to tell you what it is. You'll have to read his article. But here are a few hints.

The mutation is only common in Europeans. Asians and Africans get along just fine without it.

It's not clear whether the mutation confers selective advantage. There's some evidence that it does but it's difficult to understand why.

There are several different mutations that produce the same phenotype and it's not clear which one of them is the "most spectacular."

The article claims that the mutation appeared 10,000 years ago but that's probably not true.

The mutation has nothing to do with walking upright, opposable thumbs, big brains, or the ability to talk. Apparently those mutations are either much less spectacular or they don't qualify as "recent."

Wednesday, November 14, 2012

The Multifaith Centre at the University of Toronto is sponsoring a series of talks. I represent the control group (no faith).

The title of the series is "Is It True?" Tonight I will defend the negative position from 5:30-7:00pm in room 52 University College. If you're in Toronto, come out and participate.

Is it True? Uncovering the Heart of Each of the World's Religions

The University of Toronto Secular alliance (UTSA), in conjunction with Power 2 Change, Muslim Students Association and the Multifaith Centre is hosting a lecture and discussion series entitled "…is it true?"

Each speaker will speak on behalf of the philosophical framework to which they subscribe to. Following the lecture, there will be a period of Q and A following by an open discussion amongst attendees.

I encourage you to attend these talks as I suspect a lot of fruitful conversations can emerge. To this end, specifically, we are delighted to have biochemist Dr. Larry Moran, represent our side of the conversation.

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

Disclaimer

Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.